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Protein-RNA interactions have critical roles in all aspects of gene expression. However, applying biochemical methods to understand such interactions in living tissues has been challenging. Here we develop a genome-wide means of mapping protein-RNA binding sites in vivo, by high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation(More)
BACKGROUND Higher eukaryotes express a diverse population of messenger RNAs generated by alternative splicing. Large-scale methods for monitoring gene expression must adapt in order to accurately detect the transcript variation generated by this splicing. RESULTS We have designed a high-density oligonucleotide microarray with probesets for more than one(More)
Alternative RNA splicing greatly increases proteome diversity and may thereby contribute to tissue-specific functions. We carried out genome-wide quantitative analysis of alternative splicing using a custom Affymetrix microarray to assess the role of the neuronal splicing factor Nova in the brain. We used a stringent algorithm to identify 591 exons that(More)
Alternative splicing contributes to both gene regulation and protein diversity. To discover broad relationships between regulation of alternative splicing and sequence conservation, we applied a systems approach, using oligonucleotide microarrays designed to capture splicing information across the mouse genome. In a set of 22 adult tissues, we observe(More)
Correlation of motif occurrences with gene expression intensity is an effective strategy for elucidating transcriptional cis-regulatory logic. Here we demonstrate that this approach can also identify cis-regulatory elements for alternative pre-mRNA splicing. Using data from a human exon microarray, we identified 56 cassette exons that exhibited higher(More)
MOTIVATION Many or most mammalian genes undergo alternative splicing, generating a variety of transcripts from a single gene. New information on splice variation is becoming available through technology for measuring expression levels of several exons or splice junctions per gene. We have developed a statistical method, ANalysis Of Splice VAriation (ANOSVA)(More)
permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Tissue-specific exon discovery <p>Comprehensive exon microarrays with a simple intra-gene normalization algorithm were used to detect human tissue-specific alternative splicing events, suggesting significant expression outside of known exons(More)
The body temperature of 2 persons closed off to the outside world was pergressively analyzed with a short analyzing interval showing that the spontaneous and controlling rhythms of T = 30 h are present as previously demonstrated by ASCHOFF and BLUME. The characteristic properties and differences of both curves are described. Especially it is demonstrated(More)
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